We have synthesized a cystein-rich domain in h-factor IX. This EFG-like domain contains 45 amino acids and three disulfide bonds. An extremely difficult point in this work is the definition of the peptide refolding pattern. In order to characterize this peptide and deduce the correct refolding, a series of enzymatic digestions are carried out. V8 and trypsin are used to get small pieces of peptide, that are used to map the disulfide pairings. Mass spectroscopy proves to be a very powerful tool for such S-S mapping. Most recently, we have found that matrix-assisted laser desorption ion trap mass spectrometry is particularly useful for this application to S-S mapping. (J. Qin & B.T. Chait "Rapid Accurate Identification and Characterization of Posttranslational Modifications of Proteins by MALDI Ion Trap Mass Spectrometry" Anal. Chem. 69 (1997) 4002-4009.